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- PDB-6km1: Human Carbonic Anhydrase II V143I variant 13 atm CO2 -

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Basic information

Entry
Database: PDB / ID: 6km1
TitleHuman Carbonic Anhydrase II V143I variant 13 atm CO2
ComponentsCarbonic anhydrase 2
KeywordsLYASE / carbonic anhydrase II / intermediate states / water network / point mutation
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / morphogenesis of an epithelium / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase
Similarity search - Domain/homology
BICARBONATE ION / CARBON DIOXIDE / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsKim, C.U. / Kim, J.K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2019R1A2C1004274 Korea, Republic Of
CitationJournal: Iucrj / Year: 2020
Title: Structural insights into the effect of active-site mutation on the catalytic mechanism of carbonic anhydrase.
Authors: Kim, J.K. / Lee, C. / Lim, S.W. / Andring, J.T. / Adhikari, A. / McKenna, R. / Kim, C.U.
History
DepositionJul 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Mar 3, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6106
Polymers29,3031
Non-polymers3075
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-23 kcal/mol
Surface area11850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.286, 41.446, 72.076
Angle α, β, γ (deg.)90.000, 104.181, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carbonic anhydrase 2 / / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29303.090 Da / Num. of mol.: 1 / Mutation: V143I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 364 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.3 M sodium citrate, 100 mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 30, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. obs: 106259 / % possible obs: 94.1 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 32.36
Reflection shellResolution: 1.05→1.07 Å / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 4.76 / Num. unique obs: 5079

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Processing

Software
NameVersionClassification
REFMAC5.8.0124 2015/06/02refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U7C
Resolution: 1.05→29.147 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.515 / SU ML: 0.012 / Cross valid method: FREE R-VALUE / ESU R: 0.021 / ESU R Free: 0.022
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1214 5347 -
Rwork0.1035 --
all0.104 --
obs-106239 94.083 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.403 Å2
Baniso -1Baniso -2Baniso -3
1--0.009 Å20 Å20.012 Å2
2--0.003 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.05→29.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 17 359 2426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0192394
X-RAY DIFFRACTIONr_bond_other_d0.0020.022248
X-RAY DIFFRACTIONr_angle_refined_deg2.5741.9583280
X-RAY DIFFRACTIONr_angle_other_deg1.30835248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8725316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10424.909110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.21515420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.267158
X-RAY DIFFRACTIONr_chiral_restr0.150.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212814
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02554
X-RAY DIFFRACTIONr_nbd_refined0.3280.21868
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.24134
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22126
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22054
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2130
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0090.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0530.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3610.2112
X-RAY DIFFRACTIONr_nbd_other0.3030.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2070.211
X-RAY DIFFRACTIONr_mcbond_it3.2020.8631159
X-RAY DIFFRACTIONr_mcbond_other1.510.8591158
X-RAY DIFFRACTIONr_mcangle_it3.2011.3071486
X-RAY DIFFRACTIONr_mcangle_other3.2051.3091487
X-RAY DIFFRACTIONr_scbond_it2.821.0731235
X-RAY DIFFRACTIONr_scbond_other2.8241.0741230
X-RAY DIFFRACTIONr_scangle_it3.9541.5241786
X-RAY DIFFRACTIONr_scangle_other3.9571.5241783
X-RAY DIFFRACTIONr_lrange_it6.2528.8973071
X-RAY DIFFRACTIONr_lrange_other5.1917.8992835
X-RAY DIFFRACTIONr_sphericity_free59.503565
X-RAY DIFFRACTIONr_sphericity_bonded11.75254863
X-RAY DIFFRACTIONr_rigid_bond_restr6.79934642
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.05-1.0770.1783810.1627156831190.6870.136
1.077-1.1070.1373380.1167039809791.10780.095
1.107-1.1390.1133320.0986881786291.74510.079
1.139-1.1740.1043670.0856665764192.02980.069
1.174-1.2120.1053620.0826529743292.72070.067
1.212-1.2550.13580.0796305714993.20180.067
1.255-1.3020.1033260.0786143690293.72650.066
1.302-1.3550.13150.0765974668294.11850.065
1.355-1.4150.1083020.0765771642394.55080.068
1.415-1.4840.0993430.0735481611795.21010.067
1.484-1.5640.1042860.0755272582395.44910.07
1.564-1.6590.1032420.0775054551396.06380.074
1.659-1.7730.0992550.0814761519496.5730.08
1.773-1.9140.1042180.0884471483996.90020.089
1.914-2.0960.1152540.0984087445497.4630.104
2.096-2.3420.1171840.1033773404997.72780.113
2.342-2.7010.1461620.1233365359298.19040.137
2.701-3.3010.1581460.1322843303898.38710.153
3.301-4.6390.1441180.1322146240094.33330.159
4.639-29.1470.165580.2131170137789.17940.261

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